Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001640.1 Kokia drynarioides strain JFW-HI SEQ_113282, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1670
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.39
Warning! 64 characters in sequence are not A, C, G, or T
Found at i:741 original size:216 final size:215
Alignment explanation
Indices: 261--1670 Score: 1886
Period size: 216 Copynumber: 6.6 Consensus size: 215
251 NNNNNNNNNN
* *
261 GTTCCTTAAAGTAGTCACGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
1 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
* *
326 AATCGTATCTTTTGGTCCAAATGGTTTGTCATTTTGTAAACAACCTTTTGGTCTTTAAATTT--A
66 AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTAAATTTAAA
* * * * *
389 A---A-TTACGTCAGATTTTTTCTTTTTTGGTACTTGGACGAATTTCCAAACTTGTCAAACTTTT
130 ACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTACAAACTTGTCAAACTTTT
* *
450 ACGAGTTATTTTATAACTTTG
195 ACAAGTTCTTTTATAACTTTG
* * *
471 GTTCCTTCAAGTATTCATGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCAGGA
1 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
536 AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTAAATTTAAA
66 AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAAC-TTTTGGTCTTTAAATTTAAA
** *
601 ACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTATGAACTTGTGAAACTTTT
130 ACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTACAAACTTGTCAAACTTTT
666 ACAAGTTCTTTTATAACTTTG
195 ACAAGTTCTTTTATAACTTTG
* * * ** *
687 GTTCCTTAAAGTATWCAAGATGATCCATTCMTTCGAGTAATTTTTCGAACATTCCATGCTTGGGA
1 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
* * * *
752 AATCGCATCATTTGGTCCAAATAGTTTGTCA-TTTGTAAGCAACTTTTGGTTTTTAAATTAAAAA
66 AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTTAAAA
* * * * * * *
816 CTTATTTAAGTGAGACTTGTTTCTCTTTTGGTTCTTGGATGAACTTACGAGCTTGTCAAAATGTT
131 CTTATTTACGTCAGA-TTGTTTCTCTTTTGGTTCTTGGACGAACTTACAAACTTGTCAAACTTTT
* * *
881 ACGAGTTCTTTTACAACTTCG
195 ACAAGTTCTTTTATAACTTTG
* * * * * * *
902 ATTCCTTAAAGTATTCAAAACGATCCATTCCTTTGAGCAATTTTTCAAAGCATTCCATACTCGAG
1 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCCATTTTTCGAA-CATTCCATGCTCGGG
* * **
967 AAATCGCATCATTTGGTCCAAATTAGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTGAATAAA
65 AAATCGCATCATTTGGTCCAAA-TGGTTTGTCATTTTGTAAACAAC-TTTTGGTCTTTAAATTTA
* * * *
1032 AAACTTATTTGCGTCAAAATTGTCTCTCTTTTGG-T-TTGGACGAACTTCCAAACTTGTCAAACT
128 AAACTTATTTACGTC-AGATTGTTTCTCTTTTGGTTCTTGGACGAACTTACAAACTTGTCAAACT
* * *
1095 TTTCCAAGTTATTTTATAACCTTG
192 TTTACAAGTTCTTTTATAACTTTG
* * *
1119 GTTCCTTCAAGTATTCATGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCAGGA
1 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
1184 AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAACTTTTTGGTCTTTAAATTTAAA
66 AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAAC-TTTTGGTCTTTAAATTTAAA
* * * *
1249 ACTTATTTACGTCAGATTGTTTCTTTTTTGGTACTTGGACGAATTTCCAAACTTGTCAAACTTTT
130 ACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTACAAACTTGTCAAACTTTT
* *
1314 ACGAGTTCTTTTATAACTTTT
195 ACAAGTTCTTTTATAACTTTG
* *
1335 GTTCCTTAAAGTAGTCACGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
1 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
* * * *
1400 AATCGTATCATTTGGTCCAAATGCTTTGTCATTTCGTAAACAACTTTTGGTCTTTGAATTTAAAA
66 AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTTAAAA
* * * ** * * *
1465 CTTATTTACGTCAGATTGTTCCTCTTTTGGTTCTGGGATGAACTTATGAACTTCTGAAAGTTTTA
131 CTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTACAAACTTGTCAAACTTTTA
1530 CAAGTTCTTTTATAACTTTG
196 CAAGTTCTTTTATAACTTTG
* * ** * *
1550 GTTCCTTAAAGTATTCAAGATGATCCATTCATTCGAGTAAATTTTCGAACATTCCATGCTTGGGA
1 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
** * *
1615 AATCGCATCATTTGGTCCAAATAATTTGTCA-TTTGTAAGCAACTTTTGGTTTTTAA
66 AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAA
Statistics
Matches: 1051, Mismatches: 134, Indels: 26
0.87 0.11 0.02
Matches are distributed among these distances:
209 1 0.00
210 119 0.11
212 2 0.00
214 68 0.06
215 342 0.33
216 372 0.35
217 92 0.09
218 12 0.01
219 41 0.04
220 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (215 bp):
GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGA
AATCGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAACTTTTGGTCTTTAAATTTAAAA
CTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTACAAACTTGTCAAACTTTTA
CAAGTTCTTTTATAACTTTG
Done.